Base Recalibration -Second recalibration table

Question

[priya.bmg]

Hello

I need some advice in the base recalibration step. I have build the recalibration model and have got the recalibrated bam file. To create the after model to estimate the remaining error, should I give the recalibrated bam file as input or the original bam file as input?. I am in the step to create the second recalibration table. But, not sure if the model estimates the remaining error using the recalibrated bam file.

Thanks

[alexcouzens]

I was wondering if creating the second recalibration table ('after model') was still possible.